Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1050 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0211185461 sf0211185458 2 11185461 2.61E-08 2.61E-08
vg0106597852 sf0106596852 1 6597852 2.03E-07 2.03E-07
vg0416973093 sf0416801135 4 16973093 2.72E-07 2.72E-07
vg0419558541 sf0419386576 4 19558541 6.15E-07 6.15E-07
vg0232675158 sf0232669289 2 32675158 8.55E-07 8.55E-07
vg1116285968 sf1115820841 11 16285968 1.36E-06 1.36E-06
vg1117144922 sf1116678774 11 17144922 2.88E-06 2.88E-06
vg1125341772 sf1124875612 11 25341772 3.14E-06 3.14E-06
vg0106807279 sf0106806279 1 6807279 4.84E-06 4.84E-06